Overlap matrix heatmap

Reproducing heatmap from issues/28#issuecomment-636012185

Library

library(SEtools)
library(pheatmap)
library(dplyr)
library(ComplexHeatmap)
library(RColorBrewer)
library(DT)

Data

mat <- readRDS("input/overlap_matrix.rds")

mat$isProm <- (abs(mat$distanceToTSS) < 5000) / 2 + (abs(mat$distanceToTSS) < 2500) / 2

fields <- c(
  "isProm", "diffAccessibility-logFC", "RNA_PND8_vs_PND15_logFC",
  "RNA_PND15_vs_Adult_logFC", "BS_PND7_meth", "BS_PND14_meth", "BS_PNW8_meth",
  grep("ChIP", colnames(mat), value = TRUE)
)
mat2 <- mat[, fields]
mat2 <- do.call(cbind, lapply(mat2, as.numeric))

se <- getBreaks(mat2, split.prop = 0.96, 100)
cols <- colorRampPalette(c("blue", "black", "yellow"))(101)
mat2 <- sortRows(mat2, z = FALSE)


prom <- mat2[mat2[, 1] > 0, ]
distal <- mat2[mat2[, 1] == 0, ]
pheatmap(prom,
  color = cols, breaks = se,
  cluster_cols = FALSE, cluster_rows = FALSE
)

Subset data

Level 1

# Distal
mat$isDistal <- abs(mat$distanceToTSS) > 2500

# Proximal Active
mat$isProximalActive <- !is.na(mat$RNA_PND15_vs_Adult_AveExpr)

# # Proximal Inactive
# mat$isProximalInactive <- abs(mat$RNA_PND15_vs_Adult_logFC) < 1 & mat$RNA_PND15_vs_Adult_adj.P.Val > 0.05

Level 2

mat$accUp <- mat$`diffAccessibility-logFC` > 0
# mat$accDown <- mat$`diffAccessibility-logFC` < 0

Level 3

mat$expUp <- mat$RNA_PND15_vs_Adult_logFC > 0
# mat$expDown <- mat$RNA_PND15_vs_Adult_logFC < 0

Level 4

# H3K4me3
mat$H3K4me3 <- mat$ChIP_PNW8_H3K4me3

# H3K27ac and not H3K27me or H3K4me3
mat$H3K27acOnly <- (mat$ChIP_PNW8_H3K27ac == TRUE) & (mat$ChIP_PNW8_H3K27me3 == FALSE) & (mat$ChIP_PNW8_H3K4me3 == FALSE)

# H3K27me and not H3K27ac or H3K4me3
mat$H3K27me3Only <- (mat$ChIP_PNW8_H3K27me3 == TRUE) & (mat$ChIP_PNW8_H3K27ac == FALSE) & (mat$ChIP_PNW8_H3K4me3 == FALSE)

rownames(mat) <- mat$Name

Split matrix

# select the columns according to which we want to split
mat2 <- mat[, 74:80]
# for distal sites, we don't want to look at RNA:
mat2$isProximalActive[mat2$isDistal] <- NA
mat2$expUp[mat2$isDistal] <- NA

splitAndName <- function(o) {
  s <- split(o, apply(o, 1, collapse = " ", paste))
  names(s) <- as.character(sapply(s, FUN = function(x) {
    x <- x[1, , drop = FALSE]
    y <- c(
      ifelse(x$isDistal, "distal", "proximal"),
      ifelse(x$isProximalActive, "active", "inactive"),
      ifelse(x$accUp, "accUp", "accDown"),
      ifelse(x$expUp, "rnaUp", "rnaDown")
    )
    if (!is.null(x$H3K4me3)) {
      y <- c(
        y,
        ifelse(x$H3K4me3, "H3K4me3", NA),
        ifelse(x$H3K27acOnly, "H3K27ac", NA),
        ifelse(x$H3K27me3Only, "H3K27me3", NA)
      )
    }
    paste(y[!is.na(y)], collapse = ".")
  }))
  s
}

# split without the histone marks
s1 <- splitAndName(mat2[, 1:4])
# sapply(s1, nrow)

# very fine-grained splitting, using all columns:
s2 <- splitAndName(mat2)
# sapply(s2, nrow)

s1_1 <- lapply(s1, function(x) data.frame(Name = rownames(x), x))
s2_1 <- lapply(s2, function(x) data.frame(Name = rownames(x), x))

df_s1 <- plyr::ldply(s1_1, data.frame)
colnames(df_s1)[1] <- "anno"
rownames(df_s1) <- df_s1$Name
sp_df_s1 <- split(x = df_s1, f = df_s1$anno)

df_s2 <- plyr::ldply(s2_1, data.frame)
colnames(df_s2)[1] <- "anno"
rownames(df_s2) <- df_s2$Name
sp_df_s2 <- split(x = df_s2, f = df_s2$anno)

Heatmap

Regions without ChIP data

tab_s1 <- sortRows(df_s1[, -c(1:2)], z = FALSE)

col <- c(brewer.pal(n = 3, name = "Set1")[1:2], "grey")

lgd <- Legend(
  labels = c("TRUE", "FALSE", "NA"), legend_gp = gpar(fill = col[c(2, 1, 3)]), title = "Status",
  title_gp = gpar(col = "Blue", fontsize = 14)
)

draw(
  Heatmap(
    matrix = data.matrix(df_s1[, -c(1:2)]),
    col = col,
    cluster_rows = FALSE, cluster_columns = FALSE,
    show_row_names = FALSE, row_order = rownames(tab_s1),
    row_split = df_s1$anno, name = "Regions without ChIP data", show_heatmap_legend = FALSE
  ),
  heatmap_legend_list = lgd
)

Regions with ChIP data

tab_s2 <- sortRows(df_s2[, -c(1:2)], z = FALSE)

draw(
  Heatmap(
    matrix = data.matrix(df_s2[, -c(1:2)]),
    col = col,
    cluster_rows = FALSE, cluster_columns = FALSE,
    show_row_names = FALSE, row_order = rownames(tab_s2),
    row_split = df_s2$anno, name = "Regions with ChIP data", show_heatmap_legend = FALSE
  ),
  heatmap_legend_list = lgd
)

Individual heatmaps

make_DT <- function(df) {
  df <- data.frame(df, stringsAsFactors = F, check.names = F)
  DT::datatable(
    df,
    rownames = F,
    filter = "top",
    extensions = c("Buttons", "ColReorder"),
    options = list(
      searching = FALSE,
      pageLength = 5,
      scrollX = T,
      buttons = c("copy", "csv", "excel", "pdf", "print"),
      colReorder = list(realtime = FALSE),
      dom = "fltBip",
      width = "8px", height = "5px"
    )
  )
}

Regions without ChIP data

get_col <- function(mat){
  col <- c(brewer.pal(n = 3, name = "Set1")[1:2], "grey")
  # col <- c("blue", "red", "grey")
  v <- unique(as.vector(mat))
  colors <- sapply(v, function(x){
    c <- NULL
    if(x %in% 1){
      c <- c(true = col[2])
    } else if(x %in% 0){
      c <- c(false = col[1])
    } else{
      c <- c(na = col[3])
    }
    return(c)
  })
  return(colors)
}
for (i in 1:length(sp_df_s1)) {
  
  n <- names(sp_df_s1)[i]

  cat("### ", n, "{.tabset .tabset-pills} \n\n\n")

  cat("#### Heatmap \n\n\n")
  
  m <- data.matrix(sp_df_s1[[i]][, -c(1:2)])
    
  col <- sort(get_col(m))
  
  lgd <- Legend(
  labels = toupper(names(col)), legend_gp = gpar(fill = as.character(col)), title = "Status",
  title_gp = gpar(col = "Blue", fontsize = 14)
)
  
  try(
  draw(
    Heatmap(
      matrix = m,
      col = as.character(col)[c(2,1,3)], name = "Values",
      cluster_rows = FALSE, cluster_columns = FALSE,
      column_title = n,
      show_row_names = FALSE,
      show_heatmap_legend = FALSE
    ),
    heatmap_legend_list = lgd
  )
  )
  
  cat("\n\n\n")
  
  system("mkdir -p ./output/plots/without_ChIP")
  
  pdf(file = paste0("./output/plots/without_ChIP/", n, ".pdf"), width = 11, height = 8.5)
  try(
  draw(
    Heatmap(
      matrix = m,
      col = as.character(col)[c(2,1,3)], name = "Values",
      cluster_rows = FALSE, cluster_columns = FALSE,
      column_title = n,
      show_row_names = FALSE,
      show_heatmap_legend = FALSE
    ),
    heatmap_legend_list = lgd
  )
  )
  dev.off()

  
  cat("\n\n\n")

  
  cat("#### Table \n\n\n")

  tab <- inner_join(mat[, 1:73], sp_df_s1[[i]])

  print(htmltools::tagList(make_DT(tab)))

  cat("\n\n\n")
  
  system("mkdir -p ./output/tables/without_ChIP")
  
  writexl::write_xlsx(x = tab, path = paste0("./output/tables/without_ChIP/", n, ".xlsx"), col_names = T, format_headers = T)

}

distal.accDown

Heatmap

Table

distal.accUp

Heatmap

Error : You should have at least two distinct break values.

Error : You should have at least two distinct break values.

Table

proximal.active.accDown.rnaDown

Heatmap

Table

proximal.active.accDown.rnaUp

Heatmap

Table

proximal.active.accUp.rnaDown

Heatmap

Table

proximal.active.accUp.rnaUp

Heatmap

Table

proximal.inactive.accDown

Heatmap

Error : You should have at least two distinct break values.

Error : You should have at least two distinct break values.

Table

proximal.inactive.accUp

Heatmap

Table

Regions with ChIP data

for (i in 1:length(sp_df_s2)) {
  
  n <- names(sp_df_s2)[i]

  cat("### ", n, "{.tabset .tabset-pills} \n\n\n")

  cat("#### Heatmap \n\n\n")
  
  m <- data.matrix(sp_df_s2[[i]][, -c(1:2)])
    
  col <- get_col(m)
  
  lgd <- Legend(
  labels = toupper(names(col)), legend_gp = gpar(fill = as.character(col)), title = "Status",
  title_gp = gpar(col = "Blue", fontsize = 14)
)
  try(
  draw(
    Heatmap(
      matrix = m,
      col = as.character(col), name = "Values",
      cluster_rows = FALSE, cluster_columns = FALSE,
      column_title = n,
      show_row_names = FALSE,
      show_heatmap_legend = FALSE
    ),
    heatmap_legend_list = lgd
  )
  )
  cat("\n\n\n")
  
  system("mkdir -p ./output/plots/with_ChIP")
  
  pdf(file = paste0("./output/plots/with_ChIP/", n, ".pdf"), width = 11, height = 8.5)
  try(
  draw(
    Heatmap(
      matrix = m,
      col = col, name = "Values",
      cluster_rows = FALSE, cluster_columns = FALSE,
      column_title = n,
      show_row_names = FALSE,
      show_heatmap_legend = FALSE
    ),
    heatmap_legend_list = lgd
  )
  )
  dev.off()

  cat("\n\n\n")

  cat("#### Table \n\n\n")

  tab <- inner_join(mat[, 1:73], sp_df_s2[[i]])

  print(htmltools::tagList(make_DT(tab)))

  cat("\n\n\n")
  
  system("mkdir -p ./output/tables/with_ChIP")
  
  writexl::write_xlsx(x = tab, path = paste0("./output/tables/with_ChIP/", n, ".xlsx"), col_names = T, format_headers = T)

}

distal.accDown

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

distal.accDown.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

distal.accDown.H3K27me3

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

distal.accDown.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

distal.accUp

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

distal.accUp.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

distal.accUp.H3K27me3

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

distal.accUp.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 1, 0

Table

proximal.active.accDown.rnaDown

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accDown.rnaDown.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accDown.rnaDown.H3K27me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accDown.rnaDown.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accDown.rnaUp

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accDown.rnaUp.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accDown.rnaUp.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaDown

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaDown.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaDown.H3K27me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaDown.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaUp

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaUp.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaUp.H3K27me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.active.accUp.rnaUp.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.inactive.accDown

Heatmap

Error : Values: cannot map colors to some of the levels: 0

Table

proximal.inactive.accDown.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.inactive.accDown.H3K27me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.inactive.accDown.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.inactive.accUp

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.inactive.accUp.H3K27ac

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.inactive.accUp.H3K27me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

proximal.inactive.accUp.H3K4me3

Heatmap

Error : Values: cannot map colors to some of the levels: 0, 1

Table

Save objects

save(mat, df_s1, df_s2, sp_df_s1, sp_df_s2, file = "output/overlap_tables.RData")

SessionInfo

devtools::session_info() %>%
  details::details()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.2 (2019-12-12)
 os       Ubuntu 16.04.6 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       Europe/Zurich               
 date     2020-06-12                  

─ Packages ───────────────────────────────────────────────────────────────────
 package              * version    date       lib
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 munsell                0.5.0      2018-06-12 [1]
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[1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library